R-CMD-check.yml

# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
on:
  schedule:
    - cron: "24 06 * * 1"
  workflow_dispatch:
  push:
    branches: ["*"]
    paths-ignore:
      - "Meta**"
      - "memcheck**"
      - "docs**"
      - "**.git"
      - "**.json"
      - "**.md"
      - "**.yaml"
      - "**.yml"
      - "!**R-CMD-check.yml"
      - "**.R[dD]ata"
      - "**.Rpro*"
  pull_request:
    branches: ["*"]
    paths-ignore:
      - "Meta**"
      - "memcheck**"
      - "docs**"
      - "**.git"
      - "**.json"
      - "**.md"
      - "**.yaml"
      - "**.yml"
      - "!**R-CMD-check.yml"
      - "**.R[dD]ata"
      - "**.Rpro*"

name: R-CMD-check

jobs:
  check-release:
    runs-on: ubuntu-24.04
    name: ubuntu-24.04 (release)

    env:
      _R_CHECK_CRAN_INCOMING_: true # Seemingly not set by --as-cran
      _R_CHECK_FORCE_SUGGESTS_: false # CRAN settings
      R_COMPILE_AND_INSTALL_PACKAGES: 'never'
      _R_CHECK_THINGS_IN_CHECK_DIR_: false
      R_REMOTES_STANDALONE: true
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: "https://packagemanager.posit.co/cran/__linux__/noble/latest"
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - name: Checkout git repo
        uses: actions/checkout@v6

      - name: Temporarily bump package version
        run: |
          old_version=$(grep "Version:" DESCRIPTION | awk '{print $2}')
          if [[ $(echo "$old_version" | tr -cd '.' | wc -c) -eq 2 ]]; then
            new_version="${old_version}.8888"
            if [[ "$RUNNER_OS" == "macOS" ]]; then
              sed -i "" "s/Version: .*/Version: ${new_version}/" DESCRIPTION
            else
              sed -i "s/Version: .*/Version: ${new_version}/" DESCRIPTION
            fi
          fi
        shell: bash
        
      - name: Set up R
        uses: r-lib/actions/setup-r@v2

      - name: Set up R dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          cache-version: 2-${{ runner.arch }}
          extra-packages: |
            ms609/TreeDistData
          needs: |
            check

      - name: Check package
        uses: r-lib/actions/check-r-package@v2


  check-all:
    runs-on: ${{ matrix.config.os }}
    name: ${{ matrix.config.os }} (${{ matrix.config.r }})

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: windows-latest, r: "release"}
          - {os: macos-15-intel, r: "release"} # Until Intel architecture retired 2027-11
          - {os: macOS-latest, r: "release"}
          - {os: ubuntu-22.04, r: '4.1', rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest"}
          - {os: ubuntu-24.04-arm, r: "release", rspm: "https://packagemanager.posit.co/cran/__linux__/noble/latest"}
          - {os: ubuntu-24.04, r: "devel", rspm: "https://packagemanager.posit.co/cran/__linux__/noble/latest"}

    env:
      _R_CHECK_CRAN_INCOMING_: ${{ github.event_name == 'pull_request' }}
      _R_CHECK_FORCE_SUGGESTS_: false # CRAN settings
      R_COMPILE_AND_INSTALL_PACKAGES: 'never'
      _R_CHECK_THINGS_IN_CHECK_DIR_: false
      R_REMOTES_STANDALONE: true
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      R_REALLY_FORCE_SYMBOLS: true # Until R4.3
      RSPM: ${{ matrix.config.rspm }}
      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - name: Checkout git repo
        uses: actions/checkout@v6

      - name: Temporarily bump package version
        run: |
          old_version=$(grep "Version:" DESCRIPTION | awk '{print $2}')
          if [[ $(echo "$old_version" | tr -cd '.' | wc -c) -eq 2 ]]; then
            new_version="${old_version}.8888"
            if [[ "$RUNNER_OS" == "macOS" ]]; then
              sed -i "" "s/Version: .*/Version: ${new_version}/" DESCRIPTION
            else
              sed -i "s/Version: .*/Version: ${new_version}/" DESCRIPTION
            fi
          fi
        shell: bash
        
      - name: Set up R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}
          extra-repositories: https://ms609.github.io/packages/

      - name: Set up R dependencies (Windows)
        if: runner.os == 'Windows'
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          cache-version: 2-${{ runner.arch }}
          extra-packages: |
            ms609/TreeDistData
          needs: |
            check
            coverage
            
      - name: Set up R dependencies (Non-Windows)
        if: runner.os != 'Windows'
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          cache-version: 2-${{ runner.arch }}
          extra-packages: |
            ms609/TreeDistData
            phangorn=?ignore-before-r=4.4.0
            ggplot2=?ignore-before-r=4.4.0
            hypervolume=?ignore-before-r=4.4.0
            kdensity=?ignore-before-r=4.4.0
            Rogue=?ignore-before-r=4.4.0
            TreeSearch=?ignore-before-r=4.4.0
            Umatrix=?ignore-before-r=4.4.0
            uwot=?ignore-before-r=4.4.0
          needs: |
            check
        
      - name: Check package
        uses: r-lib/actions/check-r-package@v2

      - name: Code coverage
        if: runner.os == 'Windows'
        run: covr::codecov()
        shell: Rscript {0}

      - name: Notify on failure
        if: failure() && github.event_name == 'schedule'
        uses: actions/github-script@v7
        with:
          github-token: ${{ secrets.GITHUB_TOKEN }}
          script: |
            const issue_number = 164;

            const { data: comments } = await github.rest.issues.listComments({
              owner: context.repo.owner,
              repo: context.repo.repo,
              issue_number: issue_number,
              per_page: 3
            });

            const oneHourAgo = new Date(Date.now() - 60 * 60 * 1000);
            const recentFailureNotified = comments.some(comment => 
              new Date(comment.created_at) > oneHourAgo && 
              comment.body.includes('Scheduled workflow has failed')
            );
            
            if (recentFailureNotified) {
              console.log("Recently notified; don't bombard");
            } else {
              await github.rest.issues.createComment({
                owner: context.repo.owner,
                repo: context.repo.repo,
                issue_number: issue_number,
                body: 'Scheduled workflow has failed: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}'
              });
        
              await github.rest.issues.update({
                owner: context.repo.owner,
                repo: context.repo.repo,
                issue_number: issue_number,
                state: 'open'
              });
            }
  rev-dep-check:
    runs-on: ubuntu-latest
    needs: check-release

    name: revdepcheck

    env:
      R_COMPILE_AND_INSTALL_PACKAGES: 'never'
      R_REMOTES_STANDALONE: true
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: ${{ matrix.config.rspm }}
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      
    steps:
      - uses: ms609/actions/revdepcheck@main
        with:
          deps: ${{ matrix.config.deps }}
          extra-packages: ms609/TreeDistData

  benchmark:
    runs-on: ubuntu-latest
    needs: check-release
    if: github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch'
    name: benchmark

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      RSPM: "https://packagemanager.posit.co/cran/__linux__/noble/latest"
      _R_CHECK_BUILD_VIGNETTES_: false
      _R_CHECK_CRAN_INCOMING_: false
      _R_CHECK_FORCE_SUGGESTS_: false
      R_REMOTES_STANDALONE: true
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      R_REALLY_FORCE_SYMBOLS: true
      PKG_CXXFLAGS: "-O3"

    steps:
      - name: Checkout PR branch
        uses: actions/checkout@v6
        with:
          path: pr

      - name: Checkout target branch
        uses: actions/checkout@v6
        with:
          ref: ${{ github.event.pull_request.base.ref || 'main' }}
          path: main

      - name: Set up R
        uses: r-lib/actions/setup-r@v2
        with:
          extra-repositories: https://ms609.github.io/packages/

      - name: Install R dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          dependencies: '"hard"'
          extra-packages: |
            github::ms609/TreeTools
          needs: benchmark

      - name: Benchmark PR
        uses: ms609/actions/benchmark-step@main
        with:
          path: pr
          output: pr

      - name: Benchmark target
        uses: ms609/actions/benchmark-step@main
        with:
          path: main
          output: main

      - name: Benchmark PR again
        uses: ms609/actions/benchmark-step@main
        with:
          path: pr
          output: pr2

      - run: dir pr-benchmark-results
        working-directory: pr
      - run: dir main-benchmark-results
        working-directory: pr

      - name: Compare benchmarks
        id: compare_results
        working-directory: pr
        run: |
          Rscript benchmark/_compare_results.R
        shell: bash

      - name: Upload PR benchmark results
        if: failure()
        uses: actions/upload-artifact@v6
        with:
          name: pr-benchmark-results
          path: pr/pr-benchmark-results/*.bench.Rds

      - name: Upload main benchmark results
        if: failure()
        uses: actions/upload-artifact@v6
        with:
          name: main-benchmark-results
          path: pr/main-benchmark-results/*.bench.Rds

      - name: Comment on PR
        if: always() && github.event_name == 'pull_request' && steps.compare_results.outputs.report != ''
        uses: actions/github-script@v7
        env:
          BENCHMARK_MESSAGE: ${{ steps.compare_results.outputs.report }}
        with:
          github-token: ${{ secrets.GITHUB_TOKEN }}
          script: |
            const benchmarkIdentifier = '<!-- benchmark-comment -->';
            const outdatedPrefix = '> **⚠️ This benchmark result is outdated. See the latest comment below.**\n\n';

            const comments = await github.rest.issues.listComments({
              owner: context.repo.owner,
              repo: context.repo.repo,
              issue_number: context.issue.number
            });

            const previousBenchmarkComments = comments.data.filter(comment =>
              comment.user.type === 'Bot' &&
              comment.body.includes(benchmarkIdentifier) &&
              !comment.body.startsWith('> **⚠️ This benchmark result is outdated.')
            );

            for (const comment of previousBenchmarkComments) {
              await github.rest.issues.updateComment({
                owner: context.repo.owner,
                repo: context.repo.repo,
                comment_id: comment.id,
                body: outdatedPrefix + comment.body
              });
            }

            const newCommentBody = benchmarkIdentifier + '\n' + process.env.BENCHMARK_MESSAGE;

            await github.rest.issues.createComment({
              owner: context.repo.owner,
              repo: context.repo.repo,
              issue_number: context.issue.number,
              body: newCommentBody
            });